1EAK | pdb_00001eak

Catalytic domain of proMMP-2 E404Q mutant

PDB DOI: https://doi.org/10.2210/pdb1EAK/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2001-07-12 Released: 2002-08-22
Deposition Author(s): Bergmann, U., Tuuttila, A., Tryggvason, K., Morgunova, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.303 (Depositor), 0.301 (DCC)
R-Value Work:
0.271 (Depositor), 0.270 (DCC)
R-Value Observed:
0.271 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Human Mmp-2 Reveals a New P

Bergmann, U., Tuuttila, A., Morgunova, E., Tryggvason, K.

To be published.

Macromolecule Content

Total Structure Weight: 191.88 kDa
Atom Count: 13,504
Modeled Residue Count: 1,693
Deposited Residue Count: 1,700
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
72 KDA TYPE IV COLLAGENASE	A, B, C, D	421	Homo sapiens	Mutation(s): 1 EC: 3.4.24.24 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08253 (Homo sapiens) Explore P08253 Go to UniProtKB: P08253
PHAROS: P08253 GTEx: ENSG00000087245
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08253
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR PEPTIDE	E [auth P], F [auth R]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	G [auth A] L [auth B] M [auth B] R [auth C] S [auth C] G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	H [auth A] I [auth A] N [auth B] O [auth B] T [auth C] H [auth A], I [auth A], N [auth B], O [auth B], T [auth C], U [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C]	AA [auth D] BA [auth D] J [auth A] K [auth A] P [auth B] AA [auth D], BA [auth D], J [auth A], K [auth A], P [auth B], Q [auth B], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.303 (Depositor), 0.301 (DCC)
R-Value Work: 0.271 (Depositor), 0.270 (DCC)
R-Value Observed: 0.271 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.67	α = 90
b = 166.15	β = 90
c = 170.13	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
ROTAPREP	data scaling
SCALA	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-08-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2016-12-21
Changes: Source and taxonomy
Version 1.3: 2018-06-13
Changes: Data collection
Version 1.4: 2019-04-03
Changes: Data collection, Source and taxonomy
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.6: 2024-10-16
Changes: Structure summary